rs10489885

Variant names:

• chr1-88803823-G-A
• rs10489885
• NM_006256.4:c.1282-568G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006256.4(PKN2):​c.1282-568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 151,940 control chromosomes in the GnomAD database, including 278 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.040 (278 hom., cov: 32)
• Consequence: PKN2 NM_006256.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 1 publications found

Genes affected

PKN2 (HGNC:9406): (protein kinase N2) Enables RNA polymerase binding activity; histone deacetylase binding activity; and protein serine/threonine kinase activity. Involved in several processes, including apical junction assembly; positive regulation of cell cycle; and positive regulation of viral genome replication. Located in several cellular components, including cleavage furrow; cytoskeleton; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904214 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006256.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2	NM_006256.4	MANE Select	c.1282-568G>A		intron	N/A	NP_006247.1	Q16513-1
	PKN2	NM_001320709.2		c.1234-568G>A		intron	N/A	NP_001307638.1	Q16513-2
	PKN2	NM_001320707.2		c.1282-1023G>A		intron	N/A	NP_001307636.1	Q16513-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2	ENST00000370521.8	TSL:1 MANE Select	c.1282-568G>A		intron	N/A	ENSP00000359552.3	Q16513-1
	PKN2	ENST00000370513.9	TSL:1	c.1282-1023G>A		intron	N/A	ENSP00000359544.5	Q16513-3
	PKN2	ENST00000866345.1		c.1324-568G>A		intron	N/A	ENSP00000536404.1

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6036 AN: 151822 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.000379

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00721

Gnomad OTH AF: 0.0240

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0399 AC: 6058 AN: 151940 Hom.: 278 Cov.: 32 AF XY: 0.0398 AC XY: 2952 AN XY: 74236

African (AFR) AF: 0.105 AC: 4346 AN: 41394

American (AMR) AF: 0.0382 AC: 583 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00664 AC: 23 AN: 3464

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5180

South Asian (SAS) AF: 0.0700 AC: 337 AN: 4812

European-Finnish (FIN) AF: 0.000379 AC: 4 AN: 10558

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00721 AC: 490 AN: 67956

Other (OTH) AF: 0.0247 AC: 52 AN: 2106

Alfa AF: 0.0226 Hom.: 38

Bravo AF: 0.0438

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		-0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10489885; hg19: chr1-89269506;